1 | // =============================================================== // |
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2 | // // |
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3 | // File : AP_codon_table.cxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Coded by Ralf Westram (coder@reallysoft.de) in January 2010 // |
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7 | // Institute of Microbiology (Technical University Munich) // |
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8 | // http://www.arb-home.de/ // |
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9 | // // |
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10 | // =============================================================== // |
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11 | |
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12 | #include "AP_codon_table.hxx" |
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13 | #include "iupac.h" |
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14 | |
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15 | #include <arbdb.h> |
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16 | |
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17 | #include <cctype> |
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18 | |
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19 | #define pn_assert(cond) arb_assert(cond) |
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20 | |
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21 | #define EMBL_BACTERIAL_TABLE_INDEX 11 |
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22 | |
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23 | // Info about translation codes was taken from |
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24 | // http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi |
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25 | |
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26 | static AWT_Codon_Code_Definition AWT_codon_def[AWT_CODON_TABLES+1] = |
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27 | { |
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28 | // 0000000001111111111222222222233333333334444444444555555555566666 |
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29 | // 1234567890123456789012345678901234567890123456789012345678901234 |
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30 | |
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31 | // "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", base1 |
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32 | // "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", base2 |
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33 | // "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG" base3 |
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34 | { |
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35 | " (1) Standard code", |
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36 | "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", // The first code in this table has to be 'Standard code'! |
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37 | "---M---------------M---------------M----------------------------", |
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38 | 1 |
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39 | }, |
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40 | { |
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41 | " (2) Vertebrate mitochondrial code", |
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42 | "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG", |
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43 | "--------------------------------MMMM---------------M------------", |
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44 | 2 |
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45 | }, |
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46 | { |
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47 | " (3) Yeast mitochondrial code", |
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48 | "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG", |
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49 | "----------------------------------MM----------------------------", |
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50 | 3 |
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51 | }, |
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52 | { |
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53 | " (4) Mold/Protozoan/Coelenterate mito. + Mycoplasma/Spiroplasma code", |
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54 | "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", |
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55 | "--MM---------------M------------MMMM---------------M------------", |
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56 | 4 |
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57 | }, |
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58 | { |
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59 | " (5) Invertebrate mitochondrial code", |
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60 | "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG", |
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61 | "---M----------------------------MMMM---------------M------------", |
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62 | 5 |
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63 | }, |
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64 | { |
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65 | " (6) Ciliate, Dasycladacean and Hexamita nuclear code", |
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66 | "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", |
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67 | "-----------------------------------M----------------------------", |
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68 | 6 |
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69 | }, |
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70 | { |
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71 | " (9) Echinoderm and Flatworm mitochondrial code", |
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72 | "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", |
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73 | "-----------------------------------M---------------M------------", |
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74 | 9 |
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75 | }, |
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76 | { |
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77 | "(10) Euplotid nuclear code", |
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78 | "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", |
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79 | "-----------------------------------M----------------------------", |
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80 | 10 |
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81 | }, |
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82 | // 0000000001111111111222222222233333333334444444444555555555566666 |
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83 | // 1234567890123456789012345678901234567890123456789012345678901234 |
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84 | |
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85 | // "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", base1 |
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86 | // "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", base2 |
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87 | // "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG" base3 |
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88 | { |
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89 | "(11) Bacterial and Plant Plastid code", |
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90 | "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", |
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91 | "---M---------------M------------MMMM---------------M------------", |
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92 | 11 |
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93 | }, |
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94 | { |
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95 | "(12) Alternative Yeast nuclear code", |
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96 | "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", |
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97 | "-------------------M---------------M----------------------------", |
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98 | 12 |
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99 | }, |
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100 | { |
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101 | "(13) Ascidian mitochondrial code", |
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102 | "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG", |
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103 | "---M------------------------------MM---------------M------------", |
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104 | 13 |
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105 | }, |
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106 | { |
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107 | "(14) Alternative Flatworm mitochondrial code", |
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108 | "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", |
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109 | "-----------------------------------M----------------------------", |
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110 | 14 |
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111 | }, |
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112 | { |
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113 | "(15) Blepharisma nuclear code", |
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114 | "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", |
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115 | "-----------------------------------M----------------------------", |
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116 | 15 |
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117 | }, |
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118 | { |
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119 | "(16) Chlorophycean mitochondrial code", |
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120 | "FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", |
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121 | "-----------------------------------M----------------------------", |
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122 | 16 |
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123 | }, |
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124 | { |
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125 | "(21) Trematode mitochondrial code", |
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126 | "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG", |
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127 | "-----------------------------------M---------------M------------", |
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128 | 21 |
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129 | }, |
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130 | { |
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131 | "(22) Scenedesmus obliquus mitochondrial code", |
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132 | "FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", |
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133 | "-----------------------------------M----------------------------", |
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134 | 22 |
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135 | }, |
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136 | { |
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137 | "(23) Thraustochytrium mitochondrial code", |
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138 | "FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", |
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139 | "--------------------------------M--M---------------M------------", |
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140 | 23 |
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141 | }, |
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142 | |
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143 | { 0, 0, 0, 0 } // end of table-marker |
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144 | }; |
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145 | |
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146 | #define MAX_EMBL_TRANSL_TABLE_VALUE 23 // maximum known EMBL transl_table value |
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147 | |
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148 | int AWT_embl_transl_table_2_arb_code_nr(int embl_code_nr) { |
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149 | // returns -1 if embl_code_nr is not known by ARB |
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150 | |
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151 | static bool initialized = false; |
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152 | static int arb_code_nr_table[MAX_EMBL_TRANSL_TABLE_VALUE+1]; // key: embl_code_nr, value: arb_code_nr or -1 |
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153 | |
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154 | if (!initialized) { |
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155 | for (int embl = 0; embl <= MAX_EMBL_TRANSL_TABLE_VALUE; ++embl) { |
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156 | arb_code_nr_table[embl] = -1; // illegal table |
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157 | } |
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158 | for (int arb_code_nr = 0; arb_code_nr < AWT_CODON_TABLES; ++arb_code_nr) { |
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159 | arb_code_nr_table[AWT_codon_def[arb_code_nr].embl_feature_transl_table] = arb_code_nr; |
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160 | } |
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161 | // should be index of 'Bacterial and Plant Plastid code' |
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162 | // (otherwise maybe AWAR_PROTEIN_TYPE_bacterial_code_index is wrong) |
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163 | pn_assert(arb_code_nr_table[EMBL_BACTERIAL_TABLE_INDEX] == AWAR_PROTEIN_TYPE_bacterial_code_index); |
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164 | pn_assert(arb_code_nr_table[1] == 0); // Standard code has to be on index zero! |
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165 | |
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166 | initialized = true; |
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167 | } |
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168 | |
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169 | if (embl_code_nr<0 || embl_code_nr>MAX_EMBL_TRANSL_TABLE_VALUE) return -1; |
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170 | |
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171 | int arb_code_nr = arb_code_nr_table[embl_code_nr]; |
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172 | #ifdef DEBUG |
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173 | if (arb_code_nr != -1) { |
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174 | pn_assert(arb_code_nr >= 0 && arb_code_nr < AWT_CODON_TABLES); |
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175 | pn_assert(AWT_arb_code_nr_2_embl_transl_table(arb_code_nr) == embl_code_nr); |
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176 | } |
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177 | #endif |
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178 | return arb_code_nr; |
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179 | } |
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180 | |
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181 | int AWT_arb_code_nr_2_embl_transl_table(int arb_code_nr) { |
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182 | pn_assert(arb_code_nr >= 0 && arb_code_nr<AWT_CODON_TABLES); |
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183 | return AWT_codon_def[arb_code_nr].embl_feature_transl_table; |
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184 | } |
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185 | |
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186 | |
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187 | static bool codon_tables_initialized = false; |
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188 | static char definite_translation[AWT_MAX_CODONS]; // contains 0 if ambiguous, otherwise it contains the definite translation |
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189 | static char *ambiguous_codons[AWT_MAX_CODONS]; // for each ambiguous codon: contains all translations (each only once) |
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190 | |
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191 | void AP_initialize_codon_tables() { |
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192 | if (codon_tables_initialized) return; |
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193 | |
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194 | int codon_nr; |
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195 | int code_nr; |
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196 | |
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197 | for (codon_nr=0; codon_nr<AWT_MAX_CODONS; codon_nr++) { |
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198 | ambiguous_codons[codon_nr] = 0; |
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199 | } |
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200 | |
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201 | pn_assert(AWT_CODON_TABLES>=1); |
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202 | memcpy(definite_translation, AWT_codon_def[0].aa, AWT_MAX_CODONS); // only one translation is really definite |
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203 | |
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204 | pn_assert(AWT_codon_def[AWT_CODON_TABLES].aa==NULL); // Error in AWT_codon_def or AWT_CODON_CODES |
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205 | |
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206 | for (code_nr=1; code_nr<AWT_CODON_TABLES; code_nr++) { |
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207 | const char *translation = AWT_codon_def[code_nr].aa; |
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208 | |
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209 | for (codon_nr=0; codon_nr<AWT_MAX_CODONS; codon_nr++) { |
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210 | if (definite_translation[codon_nr]!='?') { // is definite till now |
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211 | if (definite_translation[codon_nr]!=translation[codon_nr]) { // we found a different translation |
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212 | // create ambiguous_codons: |
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213 | char *amb = (char*)GB_calloc(AWT_MAX_CODONS+1, sizeof(char)); |
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214 | amb[0] = definite_translation[codon_nr]; |
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215 | amb[1] = translation[codon_nr]; |
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216 | |
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217 | ambiguous_codons[codon_nr] = amb; |
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218 | definite_translation[codon_nr] = '?'; |
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219 | #if defined(DEBUG) && 0 |
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220 | printf("amb[%i]='%s'\n", codon_nr, amb); |
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221 | #endif |
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222 | } |
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223 | } |
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224 | else { // is ambiguous |
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225 | if (strchr(ambiguous_codons[codon_nr], translation[codon_nr])==0) { // not listed in ambiguous codons |
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226 | // append another ambiguous codon: |
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227 | char *amb = ambiguous_codons[codon_nr]; |
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228 | amb[strlen(amb)] = translation[codon_nr]; |
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229 | #if defined(DEBUG) && 0 |
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230 | printf("amb[%i]='%s'\n", codon_nr, amb); |
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231 | #endif |
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232 | } |
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233 | } |
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234 | } |
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235 | } |
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236 | |
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237 | codon_tables_initialized = true; |
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238 | } |
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239 | |
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240 | // return 0..3 (ok) or 4 (failure) |
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241 | inline int dna2idx(char c) { |
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242 | switch (c) { |
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243 | case 'T': case 't': |
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244 | case 'U': case 'u': return 0; |
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245 | case 'C': case 'c': return 1; |
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246 | case 'A': case 'a': return 2; |
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247 | case 'G': case 'g': return 3; |
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248 | } |
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249 | return 4; |
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250 | } |
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251 | |
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252 | inline char idx2dna(int idx) { |
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253 | pn_assert(idx>=0 && idx<4); |
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254 | return "TCAG"[idx]; |
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255 | } |
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256 | |
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257 | inline int calc_codon_nr(const char *dna) { |
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258 | int i1 = dna2idx(dna[0]); |
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259 | int i2 = dna2idx(dna[1]); |
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260 | int i3 = dna2idx(dna[2]); |
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261 | |
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262 | if (i1==4||i2==4||i3==4) return AWT_MAX_CODONS; // is not a codon |
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263 | |
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264 | int codon_nr = i1*16 + i2*4 + i3; |
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265 | pn_assert(codon_nr>=0 && codon_nr<=AWT_MAX_CODONS); |
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266 | return codon_nr; |
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267 | } |
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268 | |
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269 | inline void build_codon(int codon_nr, char *to_buffer) { |
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270 | pn_assert(codon_nr>=0 && codon_nr<AWT_MAX_CODONS); |
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271 | |
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272 | to_buffer[0] = idx2dna((codon_nr>>4)&3); |
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273 | to_buffer[1] = idx2dna((codon_nr>>2)&3); |
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274 | to_buffer[2] = idx2dna(codon_nr&3); |
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275 | } |
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276 | |
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277 | const char* AWT_get_codon_code_name(int code) { |
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278 | pn_assert(code>=0 && code<AWT_CODON_TABLES); |
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279 | return AWT_codon_def[code].name; |
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280 | } |
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281 | |
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282 | static const char *protein_name[26+1] = { |
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283 | "Ala", // A |
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284 | "Asx", // B |
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285 | "Cys", // C |
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286 | "Asp", // D |
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287 | "Glu", // E |
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288 | "Phe", // F |
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289 | "Gly", // G |
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290 | "His", // H |
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291 | "Ile", // I |
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292 | 0, // J |
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293 | "Lys", // K |
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294 | "Leu", // L |
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295 | "Met", // M |
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296 | "Asn", // N |
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297 | 0, // O |
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298 | "Pro", // P |
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299 | "Gln", // Q |
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300 | "Arg", // R |
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301 | "Ser", // S |
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302 | "Thr", // T |
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303 | 0, // U |
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304 | "Val", // V |
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305 | "Trp", // W |
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306 | "Xxx", // X |
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307 | "Tyr", // Y |
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308 | "Glx", // Z |
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309 | 0 |
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310 | }; |
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311 | |
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312 | const char *AP_get_protein_name(char protein) { |
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313 | if (protein=='*') return "End"; |
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314 | if (protein=='-') return "---"; |
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315 | |
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316 | pn_assert(protein>='A' && protein<='Z'); |
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317 | pn_assert(protein_name[protein-'A']!=0); |
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318 | return protein_name[protein-'A']; |
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319 | } |
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320 | |
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321 | #ifdef DEBUG |
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322 | |
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323 | inline char nextBase(char c) { |
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324 | switch (c) { |
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325 | case 'T': return 'C'; |
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326 | case 'C': return 'A'; |
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327 | case 'A': return 'G'; |
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328 | case 'G': return 0; |
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329 | default: pn_assert(0); |
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330 | } |
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331 | return 0; |
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332 | } |
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333 | |
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334 | void AWT_dump_codons() { |
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335 | AWT_allowedCode allowed_code; |
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336 | |
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337 | for (char c='*'; c<='Z'; c++) { |
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338 | printf("Codes for '%c': ", c); |
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339 | int first_line = 1; |
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340 | int found = 0; |
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341 | for (char b1='T'; b1; b1=nextBase(b1)) { |
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342 | for (char b2='T'; b2; b2=nextBase(b2)) { |
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343 | for (char b3='T'; b3; b3=nextBase(b3)) { |
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344 | char dna[4]; |
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345 | dna[0]=b1; |
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346 | dna[1]=b2; |
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347 | dna[2]=b3; |
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348 | dna[3]=0; |
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349 | |
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350 | AWT_allowedCode allowed_code_left; |
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351 | if (AWT_is_codon(c, dna, allowed_code, allowed_code_left)) { |
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352 | if (!first_line) printf("\n "); |
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353 | first_line = 0; |
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354 | printf("%s (", dna); |
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355 | |
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356 | int first=1; |
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357 | for (int code=0; code<AWT_CODON_TABLES; code++) { |
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358 | if (allowed_code_left.is_allowed(code)) { |
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359 | if (!first) printf(","); |
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360 | first=0; |
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361 | printf("%i", code); |
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362 | } |
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363 | } |
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364 | printf(") "); |
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365 | |
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366 | found = 1; |
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367 | } |
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368 | } |
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369 | } |
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370 | } |
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371 | if (!found) printf("none"); |
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372 | printf("\n"); |
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373 | if (c=='*') c='A'-1; |
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374 | } |
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375 | } |
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376 | #endif |
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377 | |
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378 | char AWT_is_start_codon(const char *dna, int arb_code_nr) { |
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379 | // if dna[0]..dna[2] is defined as start codon for 'arb_code_nr' |
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380 | // return 'M' (or whatever is defined in tables) |
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381 | // return 0 otherwise |
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382 | |
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383 | char is_start_codon = 0; |
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384 | int codon_nr = calc_codon_nr(dna); |
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385 | |
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386 | pn_assert(arb_code_nr >= 0 && arb_code_nr<AWT_CODON_TABLES); |
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387 | |
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388 | if (codon_nr != AWT_MAX_CODONS) { // dna is a clean codon (it contains no iupac-codes) |
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389 | const char *starts = AWT_codon_def[arb_code_nr].starts; |
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390 | |
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391 | is_start_codon = starts[codon_nr]; |
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392 | if (is_start_codon == '-') is_start_codon = 0; |
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393 | } |
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394 | |
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395 | return is_start_codon; |
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396 | } |
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397 | |
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398 | |
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399 | bool AWT_is_codon(char protein, const char *dna, const AWT_allowedCode& allowed_code, AWT_allowedCode& allowed_code_left, const char **fail_reason_ptr) { |
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400 | // return TRUE if 'dna' contains a codon of 'protein' ('dna' must not contain any gaps) |
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401 | // allowed_code contains 1 for each allowed code and 0 otherwise |
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402 | // allowed_code_left contains a copy of allowed_codes with all impossible codes set to zero |
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403 | |
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404 | pn_assert(codon_tables_initialized); |
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405 | |
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406 | const char *fail_reason = 0; |
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407 | bool is_codon = false; |
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408 | |
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409 | if (fail_reason_ptr) *fail_reason_ptr = 0; |
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410 | |
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411 | protein = toupper(protein); |
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412 | if (protein=='B') { // B is a shortcut for Asp(=D) or Asn(=N) |
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413 | is_codon = AWT_is_codon('D', dna, allowed_code, allowed_code_left, &fail_reason); |
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414 | if (!is_codon) { |
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415 | pn_assert(fail_reason != 0); // if failed there should always be a failure-reason |
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416 | char *fail1 = strdup(fail_reason); |
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417 | is_codon = AWT_is_codon('N', dna, allowed_code, allowed_code_left, &fail_reason); |
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418 | if (!is_codon) { |
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419 | char *fail2 = strdup(fail_reason); |
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420 | fail_reason = GBS_global_string("%s and %s", fail1, fail2); |
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421 | free(fail2); |
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422 | } |
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423 | free(fail1); |
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424 | } |
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425 | } |
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426 | else if (protein=='Z') { // Z is a shortcut for Glu(=E) or Gln(=Q) |
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427 | is_codon = AWT_is_codon('E', dna, allowed_code, allowed_code_left, &fail_reason); |
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428 | if (!is_codon) { |
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429 | pn_assert(fail_reason != 0); // if failed there should always be a failure-reason |
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430 | char *fail1 = strdup(fail_reason); |
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431 | is_codon = AWT_is_codon('Q', dna, allowed_code, allowed_code_left, &fail_reason); |
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432 | if (!is_codon) { |
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433 | char *fail2 = strdup(fail_reason); |
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434 | fail_reason = GBS_global_string("%s and %s", fail1, fail2); |
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435 | free(fail2); |
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436 | } |
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437 | free(fail1); |
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438 | } |
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439 | } |
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440 | else { |
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441 | int codon_nr = calc_codon_nr(dna); |
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442 | if (codon_nr==AWT_MAX_CODONS) { // dna is not a clean codon (it contains iupac-codes) |
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443 | int error_positions = 0; |
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444 | int first_error_pos = -1; |
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445 | bool too_short = false; |
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446 | { |
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447 | int iupac_pos; |
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448 | for (iupac_pos=0; iupac_pos<3 && !too_short; iupac_pos++) { |
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449 | if (!dna[iupac_pos]) { |
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450 | too_short = true; |
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451 | } |
---|
452 | else if (strchr("ACGTU", dna[iupac_pos]) == 0) { |
---|
453 | if (first_error_pos==-1) first_error_pos = iupac_pos; |
---|
454 | error_positions++; |
---|
455 | } |
---|
456 | } |
---|
457 | } |
---|
458 | |
---|
459 | if (too_short) { |
---|
460 | fail_reason = GBS_global_string("Not enough nucleotides (got '%s')", dna); |
---|
461 | } |
---|
462 | else { |
---|
463 | pn_assert(error_positions); |
---|
464 | if (error_positions==3) { // don't accept codons with 3 errors |
---|
465 | fail_reason = GBS_global_string("Three consecutive IUPAC codes '%c%c%c'", dna[0], dna[1], dna[2]); |
---|
466 | } |
---|
467 | else { |
---|
468 | const char *decoded_iupac = iupac::decode(dna[first_error_pos], GB_AT_DNA, 0); |
---|
469 | |
---|
470 | if (!decoded_iupac[0]) { // no valid IUPAC |
---|
471 | allowed_code_left.forbidAll(); |
---|
472 | fail_reason = GBS_global_string("Not a valid IUPAC code:'%c'", dna[first_error_pos]); |
---|
473 | } |
---|
474 | else { |
---|
475 | char dna_copy[4]; |
---|
476 | memcpy(dna_copy, dna, 3); |
---|
477 | dna_copy[3] = 0; |
---|
478 | |
---|
479 | #if defined(DEBUG) && 0 |
---|
480 | printf("Check if '%s' is a codon for '%c'\n", dna_copy, protein); |
---|
481 | #endif |
---|
482 | |
---|
483 | int all_are_codons = 1; |
---|
484 | AWT_allowedCode allowed_code_copy; |
---|
485 | allowed_code_copy = allowed_code; |
---|
486 | |
---|
487 | for (int i=0; decoded_iupac[i]; i++) { |
---|
488 | dna_copy[first_error_pos] = decoded_iupac[i]; |
---|
489 | if (!AWT_is_codon(protein, dna_copy, allowed_code_copy, allowed_code_left)) { |
---|
490 | all_are_codons = 0; |
---|
491 | break; |
---|
492 | } |
---|
493 | allowed_code_copy = allowed_code_left; |
---|
494 | } |
---|
495 | |
---|
496 | if (all_are_codons) { |
---|
497 | allowed_code_left = allowed_code_copy; |
---|
498 | is_codon = true; |
---|
499 | } |
---|
500 | else { |
---|
501 | allowed_code_left.forbidAll(); |
---|
502 | fail_reason = GBS_global_string("Not all IUPAC-combinations of '%s' translate", dna_copy); |
---|
503 | } |
---|
504 | #if defined(DEBUG) && 0 |
---|
505 | printf("result = %i\n", all_are_codons); |
---|
506 | #endif |
---|
507 | } |
---|
508 | } |
---|
509 | } |
---|
510 | } |
---|
511 | else if (definite_translation[codon_nr]!='?') { |
---|
512 | int ok = definite_translation[codon_nr]==protein; |
---|
513 | |
---|
514 | if (ok) { |
---|
515 | allowed_code_left = allowed_code; |
---|
516 | is_codon = true; |
---|
517 | } |
---|
518 | else { |
---|
519 | allowed_code_left.forbidAll(); |
---|
520 | fail_reason = GBS_global_string("'%c%c%c' does never translate to '%c' (1)", dna[0], dna[1], dna[2], protein); |
---|
521 | } |
---|
522 | } |
---|
523 | else if (strchr(ambiguous_codons[codon_nr], protein)==0) { |
---|
524 | allowed_code_left.forbidAll(); |
---|
525 | fail_reason = GBS_global_string("'%c%c%c' does never translate to '%c' (2)", dna[0], dna[1], dna[2], protein); |
---|
526 | } |
---|
527 | else { |
---|
528 | #if defined(ASSERTION_USED) |
---|
529 | bool correct_disallowed_translation = false; |
---|
530 | #endif |
---|
531 | |
---|
532 | // search for allowed correct translation possibility: |
---|
533 | for (int code_nr=0; code_nr<AWT_CODON_TABLES; code_nr++) { |
---|
534 | if (AWT_codon_def[code_nr].aa[codon_nr] == protein) { // does it translate correct? |
---|
535 | if (allowed_code.is_allowed(code_nr)) { // is this code allowed? |
---|
536 | allowed_code_left.allow(code_nr); |
---|
537 | is_codon = true; |
---|
538 | } |
---|
539 | else { |
---|
540 | allowed_code_left.forbid(code_nr); // otherwise forbid code in future |
---|
541 | #if defined(ASSERTION_USED) |
---|
542 | correct_disallowed_translation = true; |
---|
543 | #endif |
---|
544 | } |
---|
545 | } |
---|
546 | else { |
---|
547 | allowed_code_left.forbid(code_nr); // otherwise forbid code in future |
---|
548 | } |
---|
549 | } |
---|
550 | |
---|
551 | if (!is_codon) { |
---|
552 | pn_assert(correct_disallowed_translation); // should be true because otherwise we shouldn't run into this else-branch |
---|
553 | char left_tables[AWT_CODON_TABLES*3+1]; |
---|
554 | char *ltp = left_tables; |
---|
555 | bool first = true; |
---|
556 | for (int code_nr=0; code_nr<AWT_CODON_TABLES; code_nr++) { |
---|
557 | if (allowed_code.is_allowed(code_nr)) { |
---|
558 | if (!first) *ltp++ = ','; |
---|
559 | ltp += sprintf(ltp, "%i", code_nr); |
---|
560 | first = false; |
---|
561 | } |
---|
562 | } |
---|
563 | fail_reason = GBS_global_string("'%c%c%c' does not translate to '%c' for any of the leftover trans-tables (%s)", |
---|
564 | dna[0], dna[1], dna[2], protein, left_tables); |
---|
565 | } |
---|
566 | } |
---|
567 | } |
---|
568 | |
---|
569 | if (!is_codon) { |
---|
570 | pn_assert(fail_reason); |
---|
571 | if (fail_reason_ptr) *fail_reason_ptr = fail_reason; // set failure-reason if requested |
---|
572 | } |
---|
573 | return is_codon; |
---|
574 | } |
---|
575 | |
---|
576 | // -------------------------------------------------------------------------------- Codon_Group |
---|
577 | |
---|
578 | class Codon_Group |
---|
579 | { |
---|
580 | char codon[64]; // index is calculated with calc_codon_nr |
---|
581 | |
---|
582 | public: |
---|
583 | Codon_Group(char protein, int code_nr); |
---|
584 | ~Codon_Group() {} |
---|
585 | |
---|
586 | Codon_Group& operator += (const Codon_Group& other); |
---|
587 | int expand(char *to_buffer) const; |
---|
588 | }; |
---|
589 | |
---|
590 | Codon_Group::Codon_Group(char protein, int code_nr) { |
---|
591 | protein = toupper(protein); |
---|
592 | pn_assert(protein=='*' || isalpha(protein)); |
---|
593 | pn_assert(code_nr>=0 && code_nr<AWT_CODON_TABLES); |
---|
594 | |
---|
595 | const char *amino_table = AWT_codon_def[code_nr].aa; |
---|
596 | for (int i=0; i<AWT_MAX_CODONS; i++) { |
---|
597 | codon[i] = amino_table[i]==protein; |
---|
598 | } |
---|
599 | } |
---|
600 | |
---|
601 | Codon_Group& Codon_Group::operator+=(const Codon_Group& other) { |
---|
602 | for (int i=0; i<AWT_MAX_CODONS; i++) { |
---|
603 | codon[i] = codon[i] || other.codon[i]; |
---|
604 | } |
---|
605 | return *this; |
---|
606 | } |
---|
607 | |
---|
608 | inline int legal_dna_no(int i) { return i>=0 && i<4; } |
---|
609 | inline void my_memcpy(char *dest, const char *source, size_t length) { for (size_t l=0; l<length; l++) { dest[l] = source[l]; } } |
---|
610 | |
---|
611 | inline const char *buildMixedCodon(const char *con1, const char *con2) { |
---|
612 | int mismatches = 0; |
---|
613 | int mismatch_index = -1; |
---|
614 | static char buf[4]; |
---|
615 | |
---|
616 | for (int i=0; i<3; i++) { |
---|
617 | if (con1[i]!=con2[i]) { |
---|
618 | mismatches++; |
---|
619 | mismatch_index = i; |
---|
620 | } |
---|
621 | else { |
---|
622 | buf[i] = con1[i]; |
---|
623 | } |
---|
624 | } |
---|
625 | |
---|
626 | if (mismatches==1) { // exactly one position differs between codons |
---|
627 | pn_assert(mismatch_index!=-1); |
---|
628 | buf[mismatch_index] = iupac::combine(con1[mismatch_index], con2[mismatch_index], GB_AT_DNA); |
---|
629 | buf[3] = 0; |
---|
630 | return buf; |
---|
631 | } |
---|
632 | return 0; |
---|
633 | } |
---|
634 | |
---|
635 | static int expandMore(const char *bufferStart, int no_of_condons, char*&to_buffer) { |
---|
636 | int i, j; |
---|
637 | const char *con1, *con2; |
---|
638 | int added = 0; |
---|
639 | |
---|
640 | for (i=0; i<no_of_condons; i++) { |
---|
641 | con1 = bufferStart+3*i; |
---|
642 | |
---|
643 | for (j=i+1; j<no_of_condons; j++) { |
---|
644 | con2 = bufferStart+3*j; |
---|
645 | const char *result = buildMixedCodon(con1, con2); |
---|
646 | if (result) { |
---|
647 | to_buffer[0] = 0; |
---|
648 | // do we already have this codon? |
---|
649 | const char *found; |
---|
650 | const char *startSearch = bufferStart; |
---|
651 | for (;;) { |
---|
652 | found = strstr(startSearch, result); |
---|
653 | if (!found) break; |
---|
654 | int pos = (found-bufferStart); |
---|
655 | if ((pos%3)==0) break; // yes already here! |
---|
656 | startSearch = found+1; // was misaligned -> try behind |
---|
657 | } |
---|
658 | |
---|
659 | if (!found) { |
---|
660 | my_memcpy(to_buffer, result, 3); to_buffer+=3; |
---|
661 | added++; |
---|
662 | } |
---|
663 | } |
---|
664 | } |
---|
665 | } |
---|
666 | return no_of_condons+added; |
---|
667 | } |
---|
668 | |
---|
669 | int Codon_Group::expand(char *to_buffer) const { |
---|
670 | int count = 0; |
---|
671 | int i; |
---|
672 | char *org_to_buffer = to_buffer; |
---|
673 | |
---|
674 | for (i=0; i<AWT_MAX_CODONS; i++) { |
---|
675 | if (codon[i]) { |
---|
676 | build_codon(i, to_buffer); |
---|
677 | to_buffer += 3; |
---|
678 | count++; |
---|
679 | } |
---|
680 | } |
---|
681 | |
---|
682 | #if defined(DEBUG) && 0 |
---|
683 | to_buffer[0] = 0; |
---|
684 | printf("codons = '%s'\n", org_to_buffer); |
---|
685 | #endif |
---|
686 | |
---|
687 | for (;;) { |
---|
688 | int new_count = expandMore(org_to_buffer, count, to_buffer); |
---|
689 | if (new_count==count) break; // nothing expanded -> done |
---|
690 | count = new_count; |
---|
691 | #if defined(DEBUG) && 0 |
---|
692 | to_buffer[0] = 0; |
---|
693 | printf("codons (expandedMore) = '%s'\n", org_to_buffer); |
---|
694 | #endif |
---|
695 | } |
---|
696 | |
---|
697 | pn_assert(count==(int(to_buffer-org_to_buffer)/3)); |
---|
698 | |
---|
699 | return count; |
---|
700 | } |
---|
701 | |
---|
702 | // -------------------------------------------------------------------------------- |
---|
703 | |
---|
704 | static Codon_Group *get_Codon_Group(char protein, int code_nr) { |
---|
705 | pn_assert(code_nr>=0 && code_nr<AWT_CODON_TABLES); |
---|
706 | protein = toupper(protein); |
---|
707 | pn_assert(isalpha(protein) || protein=='*'); |
---|
708 | pn_assert(codon_tables_initialized); |
---|
709 | |
---|
710 | Codon_Group *cgroup = 0; |
---|
711 | |
---|
712 | if (protein=='B') { |
---|
713 | cgroup = new Codon_Group('D', code_nr); |
---|
714 | Codon_Group N('N', code_nr); |
---|
715 | *cgroup += N; |
---|
716 | } |
---|
717 | else if (protein=='Z') { |
---|
718 | cgroup = new Codon_Group('E', code_nr); |
---|
719 | Codon_Group Q('Q', code_nr); |
---|
720 | *cgroup += Q; |
---|
721 | } |
---|
722 | else { |
---|
723 | cgroup = new Codon_Group(protein, code_nr); |
---|
724 | } |
---|
725 | |
---|
726 | pn_assert(cgroup); |
---|
727 | |
---|
728 | return cgroup; |
---|
729 | } |
---|
730 | |
---|
731 | #define MAX_CODON_LIST_LENGTH (70*3) |
---|
732 | |
---|
733 | // get a list of all codons ("xyzxyzxyz...") encoding 'protein' in case we use Codon-Code 'code_nr' |
---|
734 | // (includes all completely contained IUPAC-encoded codons at the end of list) |
---|
735 | const char *AP_get_codons(char protein, int code_nr) { |
---|
736 | Codon_Group *cgroup = get_Codon_Group(protein, code_nr); |
---|
737 | |
---|
738 | static char buffer[MAX_CODON_LIST_LENGTH+1]; |
---|
739 | int offset = 3*cgroup->expand(buffer); |
---|
740 | pn_assert(offset<MAX_CODON_LIST_LENGTH); |
---|
741 | buffer[offset] = 0; |
---|
742 | |
---|
743 | delete cgroup; |
---|
744 | |
---|
745 | return buffer; |
---|
746 | } |
---|
747 | |
---|